In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

knitr::opts_chunk$set(echo = params$printcode, warning = FALSE, message = FALSE)

# load package
library(idepGolem)

::: {style="color: Blue"} ## If this site has contributed to your work, please cite our article: Ge, S.X., Son, E.W. & Yao, R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 19, 534 (2018). ::: ##

This html document contains what parameters values were selected on the IDEP interface of the "PCA" tab. It also includes the plots generated from those selections.

Pre-Process Summary

r params$pre_processed_descr

All PCA inputs

for (i in 1:length(params)) {
  # exclude loaded data & sample info
  if (names(params)[i] != "sample_info" && names(params)[i] != "pre_processed_data" && names(params)[i] != "all_gene_names") {
    cat(paste0(names(params)[i], ": ", params[[i]], "\n"))
  }
}

PCA plots

Principal Component Analysis

PCA_plot(
  data = params$pre_processed_data,
  sample_info = params$sample_info,
  PCAx = params$pc_x,
  PCAy = params$pc_y,
  selected_color = params$color,
  selected_shape = params$shape,
  plots_color_select = params$plots_color_select
)
pc_factor_correlation(
  data = params$pre_processed_data,
  sample_info = params$sample_info
)

Principal Component Analysis 3D

PCA_plot_3d(
  data = params$pre_processed_data,
  sample_info = params$sample_info,
  PCAx = params$pc_x,
  PCAy = params$pc_y,
  PCAz = params$pc_z,
  selected_color = params$color,
  selected_shape = params$shape,
  plots_color_select = params$plots_color_select
)

Plot not included on this report.

T-SNE

t_SNE_plot(
  data = params$pre_processed_data,
  sample_info = params$sample_info,
  selected_color = params$color,
  selected_shape = params$shape,
  plots_color_select = params$plots_color_select
)

Multi-Dimensional Scaling

MDS_plot(
  data = params$pre_processed_data,
  sample_info = params$sample_info,
  selected_color = params$color,
  selected_shape = params$shape,
  plots_color_select = params$plots_color_select
)

PCA tools tab

Biplot

PCA_biplot(
  data = params$pre_processed_data,
  sample_info = params$sample_info,
  select_gene_id = params$select_gene_id,
  all_gene_names = params$all_gene_names,
  selected_x = params$selected_x,
  selected_y = params$selected_y,
  encircle = params$encircle,
  showLoadings = params$showLoadings,
  pointlabs = params$pointlabs,
  point_size = params$point_size,
  ui_color = params$ui_color,
  ui_shape = params$ui_shape
)

Scree Plot

PCA_Scree(processed_data = params$pre_processed_data)

# PCAtools_eigencorplot(
#   processed_data = params$pre_processed_data,
#   sample_info =  params$sample_info
#       )

espors/idepGolem documentation built on Oct. 27, 2024, 4:56 a.m.